Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / analysis / AlignmentUtilsTests.java

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 1e71c41..7f7ec31 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -35,12 +35,15 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
@@ -69,14 +72,15 @@ public class AlignmentUtilsTests
       SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
       al.addSequence(s1);
     }
-    System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
+    System.out.println(new AppletFormatAdapter().formatSequences(
+            FileFormat.Clustal,
             al, true));
     for (int flnk = -1; flnk < 25; flnk++)
     {
       AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
       System.out.println("\nFlank size: " + flnk);
       System.out.println(new AppletFormatAdapter().formatSequences(
-              "Clustal", exp, true));
+              FileFormat.Clustal, exp, true));
       if (flnk == -1)
       {
         /*
@@ -209,7 +213,7 @@ public class AlignmentUtilsTests
   {
     final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
             + ">Seq1Name\nABCD\n";
-    AlignmentI al = loadAlignment(data, "FASTA");
+    AlignmentI al = loadAlignment(data, FileFormat.Fasta);
     Map<String, List<SequenceI>> map = AlignmentUtils
             .getSequencesByName(al);
     assertEquals(2, map.keySet().size());
@@ -229,11 +233,11 @@ public class AlignmentUtilsTests
    * @return
    * @throws IOException
    */
-  protected AlignmentI loadAlignment(final String data, String format)
+  protected AlignmentI loadAlignment(final String data, FileFormatI format)
           throws IOException
   {
     AlignmentI a = new FormatAdapter().readFile(data,
-            AppletFormatAdapter.PASTE, format);
+            DataSourceType.PASTE, format);
     a.setDataset(null);
     return a;
   }
@@ -1119,9 +1123,9 @@ public class AlignmentUtilsTests
     assertEquals(1, mappings.size());
 
     // map G to GGG
-    SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
+    SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
     assertEquals(1, sr.getResults().size());
-    Match m = sr.getResults().get(0);
+    SearchResultMatchI m = sr.getResults().get(0);
     assertSame(cds1Dss, m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());
@@ -1650,10 +1654,10 @@ public class AlignmentUtilsTests
     List<AlignedCodonFrame> pep1CdsMappings = MappingUtils
             .findMappingsForSequence(cds.getSequenceAt(0), pep1Mappings);
     assertEquals(1, pep1CdsMappings.size());
-    SearchResults sr = MappingUtils.buildSearchResults(pep1, 1,
+    SearchResultsI sr = MappingUtils.buildSearchResults(pep1, 1,
             pep1CdsMappings);
     assertEquals(1, sr.getResults().size());
-    Match m = sr.getResults().get(0);
+    SearchResultMatchI m = sr.getResults().get(0);
     assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());
@@ -2388,9 +2392,9 @@ public class AlignmentUtilsTests
     assertEquals(1, mappings.size());
 
     // map G to GGG
-    SearchResults sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
+    SearchResultsI sr = MappingUtils.buildSearchResults(pep3, 1, mappings);
     assertEquals(1, sr.getResults().size());
-    Match m = sr.getResults().get(0);
+    SearchResultMatchI m = sr.getResults().get(0);
     assertSame(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
     assertEquals(1, m.getStart());
     assertEquals(3, m.getEnd());